Contacts of the helix formed by residues 19 - 30 (chain D) in PDB entry 5GJQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 19 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D THR 5.6 1.8 + - - -
11D ILE 4.6 4.9 + - - -
13D SER* 3.5 32.2 - - - -
14D PRO* 5.4 1.8 - - + +
15D GLU* 5.7 2.1 - - - +
17D ARG* 3.7 33.7 + - + -
18D LEU* 1.3 75.2 - - - +
20D GLN* 1.3 60.4 + - + +
22D GLU* 3.2 13.3 + - - +
23D TYR* 2.9 66.0 + + + -
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Residues in contact with GLN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C THR* 2.8 34.8 + - - +
12C PHE* 2.8 55.3 + - - +
7D SER* 6.0 0.6 - - - -
9D THR* 4.4 31.3 + - + +
18D LEU 3.4 0.2 - - - -
19D TYR* 1.3 80.9 - - + +
21D VAL* 1.3 57.8 + - + +
23D TYR* 3.8 7.1 - - + +
24D ALA* 2.9 30.5 + - - +
128D ARG* 4.3 1.6 - - - +
129D PRO* 3.8 24.4 - - + +
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Residues in contact with VAL 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.5 34.5 - - + +
19D TYR 3.1 1.2 - - - -
20D GLN* 1.3 75.0 - - + +
22D GLU* 1.3 67.1 + - + +
24D ALA* 3.2 8.0 + - - +
25D MET* 3.0 29.0 + - + +
122D THR* 3.8 27.8 - - + -
129D PRO* 4.7 6.3 - - + -
152D PRO* 4.4 3.2 - - - +
153D SER* 3.8 35.4 - - - +
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Residues in contact with GLU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ARG* 3.3 52.6 + - + +
18D LEU 3.3 12.1 + - - +
19D TYR* 3.2 14.9 + - - +
21D VAL* 1.3 80.1 - - + +
23D TYR* 1.3 74.2 + - + +
25D MET* 3.0 14.2 + - - +
26D GLU* 3.0 25.1 + - + +
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Residues in contact with TYR 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 4.0 17.9 - - + -
13C SER 3.7 13.0 - - - +
14C PRO* 3.2 53.8 - - + +
16C GLY* 4.1 5.0 - - - -
19D TYR* 2.9 60.1 + + + +
20D GLN* 3.8 8.1 - - + +
22D GLU* 1.3 81.8 - - + +
24D ALA* 1.3 60.3 + - - +
26D GLU* 3.0 13.7 + - + +
27D ALA* 2.9 25.6 + - - +
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 4.1 22.6 - - + -
20D GLN 2.9 19.9 + - - +
21D VAL* 3.3 7.2 - - - +
23D TYR* 1.3 77.6 - - - +
25D MET* 1.3 62.1 + - - +
27D ALA* 3.0 11.4 + - - +
28D ILE* 2.9 25.9 + - - +
129D PRO* 4.6 4.7 - - + -
131D GLY* 4.4 6.3 - - - -
152D PRO* 4.0 21.1 - - + -
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Residues in contact with MET 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL* 3.0 25.2 + - + +
22D GLU* 3.0 15.5 + - - +
24D ALA* 1.3 75.2 - - - +
26D GLU* 1.3 61.9 + - - +
28D ILE* 3.2 13.7 + - + +
29D GLY* 3.0 22.7 + - - -
133D SER* 5.1 1.1 - - - +
151D ASP* 3.5 26.2 - - - +
152D PRO* 3.6 28.5 - - + -
153D SER* 5.5 1.8 - - - -
164D ILE* 6.0 3.1 - - + -
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Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PRO 4.0 18.2 - - - +
15C SER 4.8 5.2 - - - +
16C GLY* 4.6 2.2 - - - -
22D GLU* 3.0 17.0 + - + +
23D TYR* 3.0 14.9 + - + +
25D MET* 1.3 80.1 - - - +
27D ALA* 1.3 64.8 + - - +
29D GLY* 3.2 11.9 + - - +
30D HIS* 3.5 30.5 + - - +
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C PHE* 3.6 23.3 - - + -
16C GLY* 3.5 27.5 - - - +
23D TYR 2.9 9.6 + - - +
24D ALA 3.2 9.9 - - - +
26D GLU* 1.3 78.0 - - - +
28D ILE* 1.3 61.3 + - + +
30D HIS* 3.1 17.1 + - - +
31D ALA* 3.7 8.1 + - - +
78D GLY* 4.9 3.8 - - - -
79D ILE* 4.2 10.8 - - + -
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Residues in contact with ILE 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ALA 2.9 13.3 + - - +
25D MET* 3.3 16.4 - - + +
26D GLU 3.2 0.2 - - - -
27D ALA* 1.3 77.9 - - - +
29D GLY* 1.3 62.4 + - - +
31D ALA* 3.0 17.7 + - - +
77D ALA* 3.6 26.2 - - + +
78D GLY* 4.3 11.7 - - - -
131D GLY 4.3 5.4 - - - +
132D VAL 3.6 2.7 - - - +
133D SER* 3.2 41.5 - - - +
152D PRO* 3.4 28.9 - - + -
164D ILE* 4.7 6.3 - - + -
165D GLY* 3.7 16.3 - - - +
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Residues in contact with GLY 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D MET 3.0 13.0 + - - -
26D GLU* 3.2 7.6 + - - -
28D ILE* 1.3 77.2 - - - +
30D HIS* 1.3 64.4 + - - +
31D ALA 3.3 0.7 - - - -
165D GLY 4.4 9.0 - - - -
166D ASN* 3.2 31.9 - - - +
167D ASN 4.7 0.2 + - - -
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Residues in contact with HIS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C SER 3.8 23.8 + - - -
16C GLY* 5.6 0.9 - - - -
26D GLU* 3.7 23.3 + - - +
27D ALA* 3.1 10.8 + - - +
28D ILE 3.1 1.4 - - - -
29D GLY* 1.3 83.1 + - - +
31D ALA* 1.3 60.3 + - - +
50D ARG* 3.6 19.5 + - - +
166D ASN* 5.0 3.5 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il